If it was me I'd be looking at the switch under the shifter, or the servo and linkage for the single disc diaphragm clutch... or the clutch itself. The automatic stick shift does have a converter that transfers the power of the engine to the transmission, but when you grasp the shift lever it activates a switch that engages a servo that releases a standard single plate dry clutch. If this is not working properly it will be extremely hard to shift. As far as changing to over to a standard trans... once again if it was me I'd try to keep it stock and get the auto-stick working. But the change over is not that hard as there are two Beetles in my area the have had this done already. As far as the list of things you would need, I am not sure about the shift rod but everything else you have listed is a definite must.
66 Ghia, "Dexter" 76 flat window Beetle
It's not a Car it's a VolksWagon!